ATAC-seq for Characterizing Host and Pathogen Genome Accessibility During Virus Infection

Area of Science:

• Molecular Biology
• Epigenetics
• Virology

Background:

• Chromatin regulation is crucial for dynamic gene expression in biological processes and diseases.
• Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq) maps genome-wide chromatin accessibility.
• ATAC-seq is valuable for studying viral and bacterial infections, revealing pathogen replication and host defense insights.

Purpose of the Study:

• To describe an optimized ATAC-seq method for simultaneous analysis of host and viral genome accessibility.
• To investigate virus-host interactions by detecting structural changes on viral genomes.
• To provide a versatile tool for research involving foreign DNA introduction.

Main Methods:

• Utilized an optimized ATAC-seq protocol to assess chromatin accessibility.
• Applied the method to study infections with viral pathogens, specifically herpes simplex virus type I (HSV-1).
• Investigated the role of host antiviral factors in modulating viral genome accessibility.

Main Results:

• Demonstrated a systematic decrease in herpes simplex virus type I (HSV-1) genome accessibility during infection.
• Identified the host antiviral factor, interferon-gamma inducible protein 16 (IFI16), as mediating this decrease.
• Showcased the method's ability to provide mechanistic insights into virus-host interactions.

Conclusions:

• The optimized ATAC-seq protocol effectively characterizes chromatin accessibility changes in both host and viral genomes.
• IFI16 plays a role in restricting HSV-1 replication by reducing viral genome accessibility.
• This adaptable ATAC-seq method is a valuable tool for diverse research areas involving foreign DNA and host-pathogen interactions.